Mass spectrometry is a method for analyzing the mass-to-charge ratio distribution of constituents of a sample. The method uses an instrument known as a mass spectrometer, of which several different types exist. Matrix Assisted Laser Desorption and Ionization-Time of Flight (MALDI-ToF) mass spectrometers are commonly used in the life sciences. In MALDI-ToF, a sample/matrix mixture is placed on a defined location (spot) on a metal plate, known as a MALDI plate. A UV laser beam is directed onto a location in the spot for a very brief instant (known as a “shot”), causing desorption and ionization of molecules or other constituents of the sample. The sample components “fly” to a mass spectrometer detector due to the presence of an electric field. The instrument measures mass to charge ratio (m/z) and intensity of the components in the sample and generates the results in the form of a spectrum.
Typically, in a MALDI-ToF measurement, there are several hundred shots applied to each spot on the MALDI plate and the resulting spectra (each shot produces one spectrum) are summed to produce an overall mass spectrum. U.S. Pat. No. 7,109,491 discloses representative MALDI plates used in MALDI-TOF mass spectrometry. The plates include a multitude of individual locations or spots where the sample is applied to the plate, typically arranged in an array of perhaps several hundred such spots. Mass spectrometers for performing MALDI-ToF are available from a number of different manufacturers, and persons skilled in the art are familiar with their basic design and function. In this document, we use the terms “machine”, “mass spectrometer” and “instrument” interchangeably.
Mass spectrometry has many uses in the life and physical sciences. One of the uses is to classify a sample into one or more groups based on the similarity of features in a mass spectrum obtained from the sample to a reference spectrum, or collection of reference spectra, with the aid of a computer-implemented classifier. One example of this use is a test of the applicant's assignee, known as VERISTRAT®. This test is a MALDI-ToF mass spectrometry serum-based test that has clinical utility in the patient selection for specific targeted therapies for treatment of solid epithelial tumors. See U.S. Pat. No. 7,736,905, the content of which is incorporated by reference herein, which describes the test in detail. In brief, a mass spectrum of a serum sample of a patient is obtained. After certain pre-processing steps are performed on the spectrum, the spectrum is compared with a training (or reference) set of class-labeled spectra of other cancer patients with the aid of a computer programmed as a classifier. The class-labeled spectra are associated with two classes of patients: those that benefitted from treatment with epidermal growth factor receptor inhibitors (EGFRIs), class label of “Good”, and those that did not, class label of “Poor”. The classifier assigns a class label to the spectrum under test. The class label for the sample under test is either “Good” or “Poor,” or in rare cases where the classification test fails the class label for the sample is deemed “indeterminate.”
A given mass spectrometer used in classification of samples, such as for example in the VERISTRAT test, may be subject to periodic adjustments, replacement of parts or other maintenance or service as incident to the normal use and wear and tear on the machine. Additionally, the machine itself may be subject to performance drift over time. These adjustments, replacements of parts, maintenance or service, as well as performance drift, can cause the instrument itself to produce a spectrum from a given sample which may exhibit slight, but still significant, changes relative to another spectrum produced from the very same sample prior to the service, maintenance or replacement of parts, or at some earlier point in time. These changes may affect the accuracy of the test, and could, in theory, cause the test to produce an incorrect class label for the sample.
Hence, there is therefore a need for validating or “qualifying” the performance of a mass spectrometer so as to ensure that the spectra produced from samples after service, maintenance or replacement of parts, or over the course of time, are consistently and reliably classified. This invention meets that need.
Previous machine qualification protocols for mass spectrometers have been based on a subjective assessment of spectra produced by standardized preparations of known proteins in known concentrations. The article of Cairns et al., Integrated multi-level quality control for proteomic profiling studies using mass spectrometry, BMC Bioinformatics 2008 9:519, describes a quality control process to allow for the identification of low quality spectra reliably. The present applicants have also used feature concordance plots to qualify mass spectrometer performance. Feature concordance plots are plots of the intensity of individual selected features (peaks, e.g., peaks used for classification) in two sets of spectra (e.g., obtained from two aliquots of the same sample before and after maintenance or service). Human evaluation of the plots is used to determine if the machine performance meets a standard of “qualification” or “validation.” This prior art method is inadequate, because it requires prior experience and expertise in analyzing the spectra and peaks used in the concordance plot, and the process involves a subjective assessment of the quality of concordance.
In this disclosure, a method is provided for a fully-specified, objective, and automated approach to evaluation of mass spectrometry machine performance.